This is an overview of the thirteenth edition of the BioASQ challenge in the context of the Conference and Labs of the Evaluation Forum (CLEF) 2025. BioASQ is a series of international challenges promoting advances in large-scale biomedical semantic indexing and question answering. This year, BioASQ consisted of new editions of the two established tasks, b and Synergy, and four new tasks: a) Task MultiClinSum on multilingual clinical summarization. b) Task BioNNE-L on nested named entity linking in Russian and English. c) Task ELCardioCC on clinical coding in cardiology. d) Task GutBrainIE on gut-brain interplay information extraction. In this edition of BioASQ, 83 competing teams participated with more than 1000 distinct submissions in total for the six different shared tasks of the challenge. Similar to previous editions, several participating systems achieved competitive performance, indicating the continuous advancement of the state-of-the-art in the field.

This is an overview of the twelfth edition of the BioASQ challenge in the context of the Conference and Labs of the Evaluation Forum (CLEF) 2024. BioASQ is a series of international challenges promoting advances in large-scale biomedical semantic indexing and question answering. This year, BioASQ consisted of new editions of the two established tasks b and Synergy, and two new tasks: a) MultiCardioNER on the adaptation of clinical entity detection to the cardiology domain in a multilingual setting, and b) BIONNE on nested NER in Russian and English. In this edition of BioASQ, 37 competing teams participated with more than 700 distinct submissions in total for the four different shared tasks of the challenge. Similarly to previous editions, most of the participating systems achieved competitive performance, suggesting the continuous advancement of the state-of-the-art in the field.

This thesis work falls within the framework of question answering (QA) in the biomedical domain where several specific challenges are addressed, such as specialized lexicons and terminologies, the types of treated questions, and the characteristics of targeted documents. We are particularly interested in studying and improving methods that aim at finding accurate and short answers to biomedical natural language questions from a large scale of biomedical textual documents in English. QA aims at providing inquirers with direct, short and precise answers to their natural language questions. In this Ph.D. thesis, we propose four contributions to improve the performance of QA in the biomedical domain. In our first contribution, we propose a machine learning-based method for question type classification to determine the types of given questions which enable to a biomedical QA system to use the appropriate answer extraction method. We also propose an another machine learning-based method to assign one or more topics (e.g., pharmacological, test, treatment, etc.) to given questions in order to determine the semantic types of the expected answers which are very useful in generating specific answer retrieval strategies. In the second contribution, we first propose a document retrieval method to retrieve a set of relevant documents that are likely to contain the answers to biomedical questions from the MEDLINE database. We then present a passage retrieval method to retrieve a set of relevant passages to questions. In the third contribution, we propose specific answer extraction methods to generate both exact and ideal answers. Finally, in the fourth contribution, we develop a fully automated semantic biomedical QA system called SemBioNLQA which is able to deal with a variety of natural language questions and to generate appropriate answers by providing both exact and ideal answers.

This is an overview of the eleventh edition of the BioASQ challenge in the context of the Conference and Labs of the Evaluation Forum (CLEF) 2023. BioASQ is a series of international challenges promoting advances in large-scale biomedical semantic indexing and question answering. This year, BioASQ consisted of new editions of the two established tasks b and Synergy, and a new task (MedProcNER) on semantic annotation of clinical content in Spanish with medical procedures, which have a critical role in medical practice. In this edition of BioASQ, 28 competing teams submitted the results of more than 150 distinct systems in total for the three different shared tasks of the challenge. Similarly to previous editions, most of the participating systems achieved competitive performance, suggesting the continuous advancement of the state-of-the-art in the field.

This paper presents an overview of the tenth edition of the BioASQ challenge in the context of the Conference and Labs of the Evaluation Forum (CLEF) 2022. BioASQ is an ongoing series of challenges that promotes advances in the domain of large-scale biomedical semantic indexing and question answering. In this edition, the challenge was composed of the three established tasks a, b, and Synergy, and a new task named DisTEMIST for automatic semantic annotation and grounding of diseases from clinical content in Spanish, a key concept for semantic indexing and search engines of literature and clinical records. This year, BioASQ received more than 170 distinct systems from 38 teams in total for the four different tasks of the challenge. As in previous years, the majority of the competing systems outperformed the strong baselines, indicating the continuous advancement of the state-of-the-art in this domain.

Advancing the state-of-the-art in large-scale biomedical semantic indexing and question answering is the main focus of the BioASQ challenge. BioASQ organizes respective tasks where different teams develop systems that are evaluated on the same benchmark datasets that represent the real information needs of experts in the biomedical domain. This paper presents an overview of the ninth edition of the BioASQ challenge in the context of the Conference and Labs of the Evaluation Forum (CLEF) 2021. In this year, a new question answering task, named Synergy, is introduced to support researchers studying the COVID-19 disease and measure the ability of the participating teams to discern information while the problem is still developing. In total, 42 teams with more than 170 systems were registered to participate in the four tasks of the challenge. The evaluation results, similarly to previous years, show a performance gain against the baselines which indicates the continuous improvement of the state-of-the-art in this field.

In this paper, we present an overview of the eighth edition of the BioASQ challenge, which ran as a lab in the Conference and Labs of the Evaluation Forum (CLEF) 2020. BioASQ is a series of challenges aiming at the promotion of systems and methodologies for large-scale biomedical semantic indexing and question answering. To this end, shared tasks are organized yearly since 2012, where different teams develop systems that compete on the same demanding benchmark datasets that represent the real information needs of experts in the biomedical domain. This year, the challenge has been extended with the introduction of a new task on medical semantic indexing in Spanish. In total, 34 teams with more than 100 systems participated in the three tasks of the challenge. As in previous years, the results of the evaluation reveal that the top-performing systems managed to outperform the strong baselines, which suggests that state-of-the-art systems keep pushing the frontier of research through continuous improvements.

This article provides an overview of BioASQ, a new competition on biomedical semantic indexing and question answering (QA). BioASQ aims to push towards systems that will allow biomedical workers to express their information needs in natural language and that will return concise and user-understandable answers by combining information from multiple sources of different kinds, including biomedical articles, databases, and ontologies. BioASQ encourages participants to adopt semantic indexing as a means to combine multiple information sources and to facilitate the matching of questions to answers. It also adopts a broad semantic indexing and QA architecture that subsumes current relevant approaches, even though no current system instantiates all of its components. Hence, the architecture can also be seen as our view of how relevant work from fields such as information retrieval, hierarchical classification, question answering, ontologies, and linked data can be combined, extended, and applied to biomedical question answering. BioASQ will develop publicly available benchmarks and it will adopt and possibly refine existing evaluation measures. The evaluation infrastructure of the competition will remain publicly available beyond the end of BioASQ.